tests/testthat/test_diffExpressedVariants_K2RG.R

In aursiber/kissDE: Retrieves Condition-Specific Variants in RNA-Seq Data

context("diffExpressedVariants_K2RG")
test_that("diffExpressedVariants function works as expected on kissplice2refgenome file", {
  # test on kissplice2refgenome file
  fpath2 <- system.file("extdata", "output_k2rg_alt_splicing.txt", package = "kissDE")
  mySplicingcounts <- kissplice2counts(fpath2, pairedEnd = TRUE, k2rg = TRUE, counts = 2, exonicReads = FALSE)
  mySplicingconditions <- c("C1", "C1", "C2", "C2")
  diffSplicing <- diffExpressedVariants(mySplicingcounts, mySplicingconditions)
  expect_equal(names(diffSplicing), c("finalTable", "correctedPVal", "uncorrectedPVal", "resultFitNBglmModel", "f/psiTable", "k2rgFile"))
  expect_equal(dim(diffSplicing$finalTable)[2], 13)
  expect_equal(dim(diffSplicing$finalTable)[1], length(diffSplicing$correctedPVal))
  expect_equal(dim(diffSplicing$finalTable)[1], dim(diffSplicing$`f/psiTable`)[1])
  expect_equal(names(diffSplicing$correctedPVal), names(diffSplicing$uncorrectedPVal))
  expect_equal(names(diffSplicing$correctedPVal), rownames(diffSplicing$resultFitNBglmModel))
  expect_match(diffSplicing$k2rgFile, "output_k2rg_alt_splicing.txt")
  expect_equal(dim(diffSplicing$finalTable[which(diffSplicing$finalTable$Adjusted_pvalue <= 0.05),])[1], 18)
  expect_equal(diffSplicing$finalTable[which(diffSplicing$finalTable$ID == "bcc_144389|Cycle_0"), "Deltaf/DeltaPSI"], 0.6487)
})